gnu: seqmagick: Update to 0.7.0.

* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.7.0.  Use
python-3.
[arguments]: Remove replacement phase for check.
[inputs]: Add biopython.  Remove python2-biopython-1.66.
(python2-biopython-1.66): Remove variable.
master
Ben Woodcroft 2018-01-09 22:18:06 +10:00
parent 5424f9bcab
commit 39fb853abe
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GPG Key ID: 2A6AD9F4AAC20DF6
1 changed files with 4 additions and 31 deletions

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@ -790,20 +790,6 @@ into separate processes; and more.")
(define-public python2-biopython
(package-with-python2 python-biopython))
;; An outdated version of biopython is required for seqmagick, see
;; https://github.com/fhcrc/seqmagick/issues/59
;; When that issue has been resolved this package should be removed.
(define python2-biopython-1.66
(package
(inherit python2-biopython)
(version "1.66")
(source (origin
(method url-fetch)
(uri (pypi-uri "biopython" version))
(sha256
(base32
"1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp"))))))
(define-public bpp-core
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
@ -5391,7 +5377,7 @@ bioinformatics file formats, sequence alignment, and more.")
(define-public seqmagick
(package
(name "seqmagick")
(version "0.6.1")
(version "0.7.0")
(source
(origin
(method url-fetch)
@ -5400,25 +5386,12 @@ bioinformatics file formats, sequence alignment, and more.")
version ".tar.gz"))
(sha256
(base32
"0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d"))))
"12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
(build-system python-build-system)
(arguments
;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
;; Current test in setup.py does not work as of 0.6.1,
;; so use nose to run tests instead for now. See
;; https://github.com/fhcrc/seqmagick/issues/55
(replace 'check (lambda _ (zero? (system* "nosetests")))))))
(inputs
;; biopython-1.66 is required due to
;; https://github.com/fhcrc/seqmagick/issues/59
;; When that issue is resolved the 'python2-biopython-1.66' package
;; should be removed.
`(("python-biopython" ,python2-biopython-1.66)))
`(("python-biopython" ,python-biopython)))
(native-inputs
`(("python-nose" ,python2-nose)))
`(("python-nose" ,python-nose)))
(home-page "https://github.com/fhcrc/seqmagick")
(synopsis "Tools for converting and modifying sequence files")
(description